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<title>Generic Genome Browser</title>
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<h1>Generic Genome Browser, v2, VirtualBox Edition</h1>

<a href="http://www.gmod.org/"><img src="gmod_cog.jpeg" border="0" align="RIGHT"></a>

<p>

Welcome to the Generic Genome Browser, VirtualBox Edition!

<h2>Documentation</h2>

<dl>
  <dt><b>Online tutorial and sample data files</b></dt>
  <dd><a href="tutorial/tutorial.html">/var/www/gbrowse2/tutorial<a>.</dd>
  <dt><b>Installation and configuration manual</b></dt>
  <dd><b><a href="http://gmod.org/wiki/GBrowse_2.0_HOWTO">GBrowse 2.0 HOWTO</a></b></dd>
  <dt><b>Example scripts to control GBrowse from the command line</b></dt>
  <dd><a href="example_scripts">/var/www/gbrowse2/example_scripts</a></dd>
</dl>

<h2>Example Databases</h2>

<p>

A few "starter" databases have been installed for you. You can access
them from within the virtual machine
at <a href="http://localhost/fgb2/gbrowse">http://localhost/fgb2/gbrowse</a>,
or from outside the virtual machine using
http://host.machine:8081/fgb2/gbrowse, where "host.machine" is the DNS
name or IP address of the computer that is hosting VirtualBox.

<ul>
<li><a href="/fgb2/gbrowse/sacCer3">S. cerevisiae genome (April 2011), genes and DNA</a></li>
<li><a href="/fgb2/gbrowse/ce10">C. elegans genome (WS220), genes and DNA</a></li>
<li><a href="/fgb2/gbrowse/yeast_advanced">S. cerevisiae, advanced example (chromosomes 1+2 only)</a></li>
</ul>

<p>

More starter databases can be installed by running the command line
script "gbrowse_import_ucsc_db.pl". Genome builds are selected using
the <a href="genome.ucsc.edu">UCSC genome browser</a> build name.
For example, to load the human genome:

 gbrowse_import_ucsc_db.pl hg19 'H. sapiens genome (hg19), genes and DNA'

<h2>Directory Paths</h2>

<p>

For future reference, here is where you've installed GBrowse's various
components:

<dl>
  <dt>GBrowse documentation, stylesheets and in-memory databases.
  <dd><b>/opt/gbrowse/var/www/gbrowse2</b>
      <p>
  <dt>GBrowse configuration files
  <dd><b>/opt/gbrowse/etc</b>
      <p>
  <dt>Preinstalled sample database(s)
  <dd><b>/opt/gbrowse/lib/gbrowse2/databases</b>
      <p>
  <dt>GBrowse CGI (web) scripts
  <dd><ul>
          <li><b>/usr/lib/cgi-bin/gb2/gbrowse</b>
          <li><b>/usr/lib/cgi-bin/gb2/gbrowse_img</b>
          <li><b>/usr/lib/cgi-bin/gb2/gbrowse_details</b>
      </ul>
      <p>
  <dt>Temporary directories for cached images and sessions.
  <dd><b>/tmp/gbrowse2</b>
</dl>

<p>

<h2>Learning More</h2>

<p>

To find out more about Gbrowse, try the:

<ul>
  <li><a href="http://gmod.org/wiki/GBrowse_2.0_HOWTO">GBrowse 2.0 HOWTO</a>
  <li><a href="tutorial/tutorial.html">GBrowse Tutorial</a>
 <!-- <li><a href="contrib/conf_files">Sample Configuration Files</a> -->
</ul>


<hr>
<address>Lincoln D. Stein, lstein@cshl.org<br>
<a href="http://www.cshl.org/">Cold Spring Harbor Laboratory</a></address>
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Last modified: Thu Mar 18 18:59:16 PDT 2010
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